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r144: adjust primary aln after cigar

This commit is contained in:
Heng Li 2017-07-02 22:43:02 -04:00
parent 2b45ba7a0b
commit 632b8638d2
3 changed files with 27 additions and 3 deletions
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26
hit.c
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@ -109,6 +109,28 @@ void mm_update_parent(void *km, float mask_level, int n, mm_reg1_t *r) // due to
if (j == k) w[k++] = i; if (j == k) w[k++] = i;
} }
kfree(km, w); kfree(km, w);
for (i = 0; i < n; ++i) {
mm_reg1_t *ri = &r[i], *rp, tmp;
int t;
if (ri->p == 0 || ri->id == ri->parent || ri->parent < 0) continue;
rp = &r[ri->parent];
if (rp->p && ri->p->dp_max > rp->p->dp_max) {
ri->subsc = rp->score;
tmp = *ri, *ri = *rp, *rp = tmp;
t = ri->id, ri->id = rp->id, rp->id = t;
t = ri->parent, ri->parent = rp->parent, rp->parent = t;
}
}
for (i = 0; i < n; ++i) {
mm_reg1_t *ri = &r[i], *rp;
if (ri->id == ri->parent || ri->parent < 0) continue;
rp = &r[ri->parent];
rp->subsc = rp->subsc > ri->score? rp->subsc : ri->score;
if (rp->p && ri->p)
rp->p->dp_max2 = rp->p->dp_max2 > ri->p->dp_max? rp->p->dp_max2 : ri->p->dp_max;
}
} }
void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,parent} in sync; also reset id void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,parent} in sync; also reset id
@ -255,7 +277,9 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs)
mm_reg1_t *r = &regs[i]; mm_reg1_t *r = &regs[i];
if (r->parent == r->id) { if (r->parent == r->id) {
int mapq; int mapq;
mapq = (int)(30.0 * (1. - (float)r->subsc / r->score) * logf(r->score)); if (r->p && r->p->dp_max2 > 0 && r->p->dp_max > 0)
mapq = (int)(30.0 * (1. - (float)(r->p->dp_max2 * r->subsc) / (r->p->dp_max * r->score)) * logf(r->score));
else mapq = (int)(30.0 * (1. - (float)r->subsc / r->score) * logf(r->score));
mapq = mapq > 0? mapq : 0; mapq = mapq > 0? mapq : 0;
r->mapq = mapq < 60? mapq : 60; r->mapq = mapq < 60? mapq : 60;
} else r->mapq = 0; } else r->mapq = 0;

2
main.c
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@ -10,7 +10,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r143-pre" #define MM_VERSION "2.0-r144-pre"
void liftrlimit() void liftrlimit()
{ {

2
minimap.h
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@ -45,7 +45,7 @@ typedef struct {
typedef struct { typedef struct {
uint32_t capacity; uint32_t capacity;
int32_t dp_score, dp_max; int32_t dp_score, dp_max, dp_max2;
uint32_t blen; uint32_t blen;
uint32_t n_diff, n_ambi; uint32_t n_diff, n_ambi;
uint32_t n_cigar; uint32_t n_cigar;